SMTL ID : 1m8v.1

Structure of Pyrococcus abyssii Sm Protein in Complex with a Uridine Heptamer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-14-mer

Ligands

7 x U- U- U- U- U- U: 5'-R(P*UP*UP*UP*UP*UP*UP*U)-3'(Non-covalent)

U-U-U-U-U-U.1: 22 residues within 4Å: Chain A: R.6, L.8, D.9, H.12, G.35, Y.36, D.37 Chain G: E.5, R.6 Chain L: R.6 Chain M: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, D.37, I.38 Chain N: D.37, H.39 Ligands: CA.8 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.2: 20 residues within 4Å: Chain B: R.6 Chain C: R.6, L.8, D.9, H.12, G.35, Y.36, D.37 Chain J: R.6 Chain K: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, D.37 Chain L: D.37, H.39 Ligands: CA.9 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.3: 20 residues within 4Å: Chain E: R.6 Chain F: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, I.38 Chain G: D.37 Chain H: R.6, L.8, D.9, H.12, G.35, Y.36, D.37 Chain N: E.5, R.6 Ligands: CA.10 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.4: 20 residues within 4Å: Chain D: R.6 Chain E: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, D.37 Chain F: D.37, H.39 Chain H: E.5, R.6 Chain I: L.8, D.9, H.12, G.35, Y.36, D.37 Ligands: CA.11 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.5: 19 residues within 4Å: Chain C: R.6 Chain D: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, D.37 Chain E: D.37 Chain I: R.6 Chain J: R.6, L.8, D.9, H.12, G.35, Y.36, D.37 Ligands: CA.12 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.6: 17 residues within 4Å: Chain A: A.4, R.6 Chain B: R.6, L.8, D.9, H.12, G.35, Y.36, D.37 Chain K: R.6 Chain L: R.6, L.8, D.9, H.12, G.35, Y.36 Ligands: CA.13 Protein-ligand interaction information (PLIP) not available U-U-U-U-U-U.7: 19 residues within 4Å: Chain A: D.37, H.39 Chain F: R.6 Chain G: R.6, P.7, L.8, D.9, H.12, G.35, Y.36, D.37 Chain M: R.6 Chain N: L.8, D.9, H.12, G.35, Y.36, D.37 Ligands: CA.14 Protein-ligand interaction information (PLIP) not available

7 x CA: CALCIUM ION(Non-functional Binders)

CA.8: 6 residues within 4Å: Ligands: U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1, U-U-U-U-U-U.1 No protein-ligand interaction detected (PLIP) CA.9: 5 residues within 4Å: Ligands: U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2, U-U-U-U-U-U.2 No protein-ligand interaction detected (PLIP) CA.10: 4 residues within 4Å: Ligands: U-U-U-U-U-U.3, U-U-U-U-U-U.3, U-U-U-U-U-U.3, U-U-U-U-U-U.3 No protein-ligand interaction detected (PLIP) CA.11: 4 residues within 4Å: Ligands: U-U-U-U-U-U.4, U-U-U-U-U-U.4, U-U-U-U-U-U.4, U-U-U-U-U-U.4 No protein-ligand interaction detected (PLIP) CA.12: 4 residues within 4Å: Ligands: U-U-U-U-U-U.5, U-U-U-U-U-U.5, U-U-U-U-U-U.5, U-U-U-U-U-U.5 No protein-ligand interaction detected (PLIP) CA.13: 4 residues within 4Å: Ligands: U-U-U-U-U.6, U-U-U-U-U.6, U-U-U-U-U.6, U-U-U-U-U.6 No protein-ligand interaction detected (PLIP) CA.14: 4 residues within 4Å: Ligands: U-U-U-U-U-U.7, U-U-U-U-U-U.7, U-U-U-U-U-U.7, U-U-U-U-U-U.7 No protein-ligand interaction detected (PLIP)

14 x U: URIDINE-5'-MONOPHOSPHATE(Non-covalent)

U.15: 9 residues within 4Å: Chain A: H.39, N.41, R.65, G.66, D.67 Chain B: R.65 Chain G: L.40 Ligands: U.16, U.21 59 PLIP interactions: 7 interactions with chain B, 8 interactions with chain F, 7 interactions with chain A, 9 interactions with chain G, 8 interactions with chain D, 6 interactions with chain H, 7 interactions with chain E, 6 interactions with chain C, 1 interactions with chain I Hydrogen bonds: B:N.41, B:N.41, B:R.65, B:R.65, B:D.67, B:D.67, F:N.41, F:N.41, F:R.65, F:R.65, F:D.67, F:D.67, A:N.41, A:N.41, A:R.65, A:R.65, A:D.67, A:D.67, G:H.39, G:N.41, G:N.41, G:R.65, G:G.66, G:D.67, D:H.39, D:N.41, D:N.41, D:R.65, D:R.65, D:D.67, D:D.67, H:N.41, H:N.41, H:R.65, H:R.65, H:D.67, E:N.41, E:N.41, E:R.65, E:R.65, E:D.67, C:N.41, C:N.41, C:R.65, C:D.67, I:R.65 pi-Stacking: B:H.39, F:H.39, A:H.39, G:H.39, D:H.39, H:H.39, E:H.39, C:H.39 Salt bridges: F:H.39, G:H.39, G:H.39, E:H.39, C:H.39 U.16: 9 residues within 4Å: Chain A: I.38, L.40 Chain B: H.39, N.41, R.65, G.66, D.67 Ligands: U.15, U.17 Protein-ligand interaction information (PLIP) not available U.17: 10 residues within 4Å: Chain B: I.38, L.40 Chain C: H.39, N.41, R.65, G.66, D.67 Chain D: R.65 Ligands: U.16, U.18 Protein-ligand interaction information (PLIP) not available U.18: 10 residues within 4Å: Chain C: I.38, L.40 Chain D: H.39, N.41, R.65, G.66, D.67 Chain E: R.65 Ligands: U.17, U.19 Protein-ligand interaction information (PLIP) not available U.19: 9 residues within 4Å: Chain D: H.39, L.40 Chain E: H.39, N.41, R.65, D.67 Chain F: R.65 Ligands: U.18, U.20 Protein-ligand interaction information (PLIP) not available U.20: 10 residues within 4Å: Chain E: H.39, L.40 Chain F: H.39, N.41, R.65, G.66, D.67 Chain G: R.65 Ligands: U.19, U.21 Protein-ligand interaction information (PLIP) not available U.21: 11 residues within 4Å: Chain A: R.65 Chain F: I.38, H.39, L.40 Chain G: H.39, N.41, R.65, G.66, D.67 Ligands: U.15, U.20 Protein-ligand interaction information (PLIP) not available U.22: 9 residues within 4Å: Chain H: H.39, N.41, R.65, G.66, D.67 Chain I: R.65 Chain N: L.40 Ligands: U.23, U.28 Protein-ligand interaction information (PLIP) not available U.23: 8 residues within 4Å: Chain H: L.40 Chain I: H.39, N.41, R.65, D.67 Chain J: R.65 Ligands: U.22, U.24 43 PLIP interactions: 8 interactions with chain L, 6 interactions with chain N, 6 interactions with chain I, 6 interactions with chain K, 11 interactions with chain M, 6 interactions with chain J Hydrogen bonds: L:N.41, L:N.41, L:R.65, L:R.65, L:D.67, N:N.41, N:N.41, N:R.65, N:D.67, I:N.41, I:N.41, I:R.65, I:R.65, I:D.67, K:N.41, K:N.41, K:R.65, K:D.67, M:H.39, M:N.41, M:N.41, M:R.65, M:R.65, M:D.67, M:D.67, J:N.41, J:N.41, J:R.65, J:R.65, J:D.67 Water bridges: L:D.67, M:D.67 Salt bridges: L:H.39, N:R.65, K:H.39, M:K.24, M:H.39 pi-Stacking: L:H.39, N:H.39, I:H.39, K:H.39, M:H.39, J:H.39 U.24: 9 residues within 4Å: Chain I: L.40 Chain J: H.39, N.41, R.65, G.66, D.67 Chain K: R.65 Ligands: U.23, U.25 Protein-ligand interaction information (PLIP) not available U.25: 9 residues within 4Å: Chain J: L.40 Chain K: H.39, N.41, R.65, G.66, D.67 Chain L: R.65 Ligands: U.24, U.26 Protein-ligand interaction information (PLIP) not available U.26: 10 residues within 4Å: Chain K: H.39, L.40 Chain L: H.39, N.41, R.65, G.66, D.67 Chain M: R.65 Ligands: U.25, U.27 Protein-ligand interaction information (PLIP) not available U.27: 8 residues within 4Å: Chain L: L.40 Chain M: H.39, N.41, R.65, G.66, D.67 Ligands: U.26, U.28 Protein-ligand interaction information (PLIP) not available U.28: 9 residues within 4Å: Chain M: K.24, L.40, D.67 Chain N: H.39, N.41, R.65, D.67 Ligands: U.22, U.27 Protein-ligand interaction information (PLIP) not available

Links

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Citation

Thore, S. et al., Crystal Structure of Pyrococcus abyssii Sm core and its Complex with RNA: Common Features of RNA-binding in Archaea and Eukarya. J.Biol.Chem. (2003)

Release Date

2003-02-11

Peptides

PUTATIVE SNRNP SM-LIKE PROTEIN: ABCDEFGHIJKLMN

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

H
H

I
I

J
J

K
K

L
L

M
M

N
N

PUTATIVE SNRNP SM-LIKE PROTEIN